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[r] Add initial support for ragged array writing for Seurat v5 #2523

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[r] Add initial support for ragged array writing for Seurat v5 #2523

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Commits on Sep 17, 2024

  1. [r] Add initial support for ragged array writing for Seurat v5 

    Seurat v5 adds support for ragged arrays, where not every `X` layer has
exactly the same cells and features. To handle these ragged arrays on
ingestion, re-indexing the soma join IDs is necessary to pad the `X`
layer to the full domain of the SOMA measurement

Implemented SOMA methods:
- `write_soma.Assay5()`: write a Seurat v5 assay to a SOMA measurement.
  When writing `X` layers, if a layer is ragged:
  - cast layer to `TsparseMatrix` for COO representation
  - re-index Seurat's character IDs to SOMA join IDs
  - re-index COO coordinates to SOMA join IDs
  - write array using `SOMASparseNDArray$private$.write_coo_dataframe()`

Notes:
 - This PR does not implement alternate matrix (eg. DelayedArray,
   BPCells) ingestion
    @mojaveazure
    mojaveazure committed Sep 17, 2024
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  2. Add metadata hints for v5 writing 

    Expand tests
    @mojaveazure
    mojaveazure committed Sep 17, 2024
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  3. Add new helpers to generate metadata for v5 ingestion

    @mojaveazure
    mojaveazure committed Sep 17, 2024
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  4. Update tests and docs

    @mojaveazure
    mojaveazure committed Sep 17, 2024
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  5. Add support for ragged assays

    @mojaveazure
    mojaveazure committed Sep 17, 2024
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